A perspective on physiological trade offs and finite resources for protein-expression

Together with Ralf Steuer (Humboldt-University of Berlin, Germany) we recently wrote a review for Bioessays, see https://doi.org/10.1002/bies.202300015. It addresses how we currently view the consequences of finite biosynthetic resources (for protein expression) for cellular tasks such as stress tolerance, growth and adaptation to new conditions.

We focus on Escherichia coli and Saccharomyces cerevisiae. We acknowledge that the advanced understanding we have of their physiology may not be extrapolatable to microorganisms with a qualitatively different evolutionary history. We argue that these two microorganisms optimise the expression levels of needed metabolic enzymes, given that some fraction of biosynthetic resources is allocated to proteins needed to adapt to new conditions. That latter fraction of non-growth associated protein decreases with cellular growth rate (nutrient quality) and therefore makes fast growing E. coli and S. cerevisiae cells less stress tolerant and adaptive to new nutrients. This is an example of a trade off between growth and adaptation due to finite biosynthetic resources.

If you are interested in such ideas, how they emerge from computational models, and what their precise experimental evidence is then the review we wrote might be of interest to you.

New paper: Lifestyle influences microbiome

In primate species, a change in lifestyle leads to adjustments in their microbiome. What does this mean? 

The study subject, the ARTIS gorilla Akili

Over the last years, ARTIS Micropia Professor Remco Kort and his Bioinformatics & Systems Biology student Isabel Houtkamp studied the faeces of the western lowland gorilla. They did this by comparing the composition of the microbiome of the ARTIS gorillas with that of their wild counterparts – and also with that of humans. They were assisted by Walter Pirovano and Mark Bessem of the company BaseClear, experts in the field of microbial DNA analyses. This research revealed interesting correspondences. In both primate species, a change in lifestyle led to adjustments in their microbiome. So what does this mean? 

To find out, check out their new paper here and a behind-the-scenes story Remco wrote for Micropia.